{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/113946"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/113946","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Probing small organic molecules at the angstrom-scale in the scanning transmission electron microscope","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-12-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-12-01","abstract_has_math":false,"creators":["Janicek, Blanka E"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Materials Science & Engr","degree_department":null,"school":null,"contributors":["Huang, Pinshane Y","Zuo, Jian-Min","Schleife, Andre","Murphy, Catherine J"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-04-29T21:42:51Z","date_published":"2022-04-29T21:42:51Z","updated_at":"2026-07-22T22:24:53Z","subjects":["small organic molecules","electron microscopy","scanning transmission electron microscopy","atomic-resolution imaging","electron beam damage"],"languages":["en","eng"],"rights":["Copyright 2021 Blanka E. 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Janicek"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/113946"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-12-01","The student, Blanka Janicek, accepted the attached license on 2021-08-23 at 10:47.","The student, Blanka Janicek, submitted this Dissertation for approval on 2021-08-23 at 11:04.","This Dissertation was approved for publication on 2021-08-25 at 10:59.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17114 on 2022-04-06 at 17:16:25","Made available in DSpace on 2022-04-29T21:42:51Z (GMT). No. of bitstreams: 2 JANICEK-DISSERTATION-2021.pdf: 65173568 bytes, checksum: 3e9ce1e5deebe53b25733f1e2384e10f (MD5) LICENSE.txt: 4211 bytes, checksum: bd962e75dfedf744e33d1243b4bd770e (MD5) Previous issue date: 2021-08-25","Embargo set by: Seth Robbins for item 123308 Lift date: 2024-04-29T21:43:01Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 123308 Lift date: 2024-04-29T21:44:44Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 123308 Lift date: 2024-04-29T21:46:25Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 123308 Lift date: 2024-04-29T21:47:53Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only","Small organic molecules are the foundation of chemistry, and correspondingly, unambiguous determination of their structure is essential. While scanning transmission electron microscopy (STEM) is a powerful tool for atomic-resolution structural determination, applying STEM to small organic molecules has proved challenging due to their weak electron scattering and extreme sensitivity to electron beam damage. In this thesis, we develop sample preparation, STEM imaging, and data processing techniques that enable us to directly probe the structure and arrangements of small organic molecules at the angstrom scale. We develop methods for large-scale production and deposition of samples onto ultra-low background graphene substrates, enabling the detection of the weak molecular signal. Additionally, our studies benefit from the stability provided by the graphene substrates, which increase the dose resistance of the molecules 2-6x due to their impermeability and high electrical and thermal conductivity. We then combine graphene substrates and STEM to study two technologically important small organic molecule systems: ensembles of molecules at the surface of inorganic nanoparticles and 2-dimensional (2D) molecular crystals. A longstanding challenge in nanoparticle characterization is understanding local variations in the distributions of surface molecules. We use STEM and electron energy loss spectroscopy to quantify the molecular distribution on the nanoscale, revealing up to 30% lower binding density on the ends of the particles. This anisotropy has important implications for nanoparticle synthesis and interactions, directing their growth, chemical functionalization, and colloidal assembly. Importantly, these methods enable the study of surface chemistry with site-specificity and are broadly applicable to a range of nanomaterials. An ultimate challenge in electron microscopy is to image the structure of an individual small organic molecule. We combine the protection from graphene substrates, low-dose STEM, and advanced averaging techniques to enable direct, atomic-scale imaging of 2D small organic molecule crystals. We achieve 1.3 angstrom resolution imaging a single molecule, sufficient to distinguish individual nitrogen and carbon atoms. Importantly, our methods are well-suited to analyzing nanogram quantities of material and systems for which large crystals cannot easily be grown. Our results demonstrate the potential of atomic-scale STEM as a powerful new method for structural solution of small organic molecules. Overall, this thesis demonstrates advances in sample preparation and data analysis techniques that enable nano- and atomic-scale STEM imaging of small organic molecules."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Probing small organic molecules at the angstrom-scale in the scanning transmission electron microscope"]}]}],"canonical_facts":{"dc:contributor":["Huang, Pinshane Y","Zuo, Jian-Min","Schleife, Andre","Murphy, Catherine J"],"dc:creator":["Janicek, Blanka E"],"dc:date":["2022-04-29T21:42:51Z","2024-04-29T21:47:53Z","2021-12","2021-08-25"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-12-01","The student, Blanka Janicek, accepted the attached license on 2021-08-23 at 10:47.","The student, Blanka Janicek, submitted this Dissertation for approval on 2021-08-23 at 11:04.","This Dissertation was approved for publication on 2021-08-25 at 10:59.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17114 on 2022-04-06 at 17:16:25","Made available in DSpace on 2022-04-29T21:42:51Z (GMT). No. of bitstreams: 2 JANICEK-DISSERTATION-2021.pdf: 65173568 bytes, checksum: 3e9ce1e5deebe53b25733f1e2384e10f (MD5) LICENSE.txt: 4211 bytes, checksum: bd962e75dfedf744e33d1243b4bd770e (MD5) Previous issue date: 2021-08-25","Embargo set by: Seth Robbins for item 123308 Lift date: 2024-04-29T21:43:01Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 123308 Lift date: 2024-04-29T21:44:44Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 123308 Lift date: 2024-04-29T21:46:25Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Embargo set by: Seth Robbins for item 123308 Lift date: 2024-04-29T21:47:53Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only","Small organic molecules are the foundation of chemistry, and correspondingly, unambiguous determination of their structure is essential. While scanning transmission electron microscopy (STEM) is a powerful tool for atomic-resolution structural determination, applying STEM to small organic molecules has proved challenging due to their weak electron scattering and extreme sensitivity to electron beam damage. In this thesis, we develop sample preparation, STEM imaging, and data processing techniques that enable us to directly probe the structure and arrangements of small organic molecules at the angstrom scale. We develop methods for large-scale production and deposition of samples onto ultra-low background graphene substrates, enabling the detection of the weak molecular signal. Additionally, our studies benefit from the stability provided by the graphene substrates, which increase the dose resistance of the molecules 2-6x due to their impermeability and high electrical and thermal conductivity. We then combine graphene substrates and STEM to study two technologically important small organic molecule systems: ensembles of molecules at the surface of inorganic nanoparticles and 2-dimensional (2D) molecular crystals. A longstanding challenge in nanoparticle characterization is understanding local variations in the distributions of surface molecules. We use STEM and electron energy loss spectroscopy to quantify the molecular distribution on the nanoscale, revealing up to 30% lower binding density on the ends of the particles. This anisotropy has important implications for nanoparticle synthesis and interactions, directing their growth, chemical functionalization, and colloidal assembly. Importantly, these methods enable the study of surface chemistry with site-specificity and are broadly applicable to a range of nanomaterials. An ultimate challenge in electron microscopy is to image the structure of an individual small organic molecule. We combine the protection from graphene substrates, low-dose STEM, and advanced averaging techniques to enable direct, atomic-scale imaging of 2D small organic molecule crystals. We achieve 1.3 angstrom resolution imaging a single molecule, sufficient to distinguish individual nitrogen and carbon atoms. Importantly, our methods are well-suited to analyzing nanogram quantities of material and systems for which large crystals cannot easily be grown. Our results demonstrate the potential of atomic-scale STEM as a powerful new method for structural solution of small organic molecules. Overall, this thesis demonstrates advances in sample preparation and data analysis techniques that enable nano- and atomic-scale STEM imaging of small organic molecules."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/113946"],"dc:language":["en","eng"],"dc:rights":["Copyright 2021 Blanka E. Janicek"],"dc:subject":["small organic molecules","electron microscopy","scanning transmission electron microscopy","atomic-resolution imaging","electron beam damage"],"dc:title":["Probing small organic molecules at the angstrom-scale in the scanning transmission electron microscope"],"dc:type":["text"],"thesis:degree_discipline":["Materials Science & Engr"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:53Z"}